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Detection of genes with atypical nucleotide sequence in microbial genomes
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
2002 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 54, no 3, 365-375 p.Article in journal (Refereed) Published
Abstract [en]

Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures. In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that genes from different genomes can be separated with a high degree of accuracy, according to these distance values. In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides, we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects. Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.

Place, publisher, year, edition, pages
2002. Vol. 54, no 3, 365-375 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-90105DOI: 10.1007/s00239-001-0051-8PubMedID: 11847562OAI: oai:DiVA.org:uu-90105DiVA: diva2:162310
Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2017-12-14Bibliographically approved
In thesis
1. Dynamics of Microbial Genome Evolution
Open this publication in new window or tab >>Dynamics of Microbial Genome Evolution
2003 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The success of microbial life on Earth can be attributed not only to environmental factors, but also to the surprising hardiness, adaptability and flexibility of the microbes themselves. They are able to quickly adapt to new niches or circumstances through gene evolution and also by sheer strength of numbers, where statistics favor otherwise rare events.

An integral part of adaptation is the plasticity of the genome; losing and acquiring genes depending on whether they are needed or not. Genomes can also be the birthplace of new gene functions, by duplicating and modifying existing genes. Genes can also be acquired from outside, transcending species boundaries. In this work, the focus is set primarily on duplication, deletion and import (lateral transfer) of genes – three factors contributing to the versatility and success of microbial life throughout the biosphere.

We have developed a compositional method of identifying genes that have been imported into a genome, and the rate of import/deletion turnover has been appreciated in a number of organisms. Furthermore, we propose a model of genome evolution by duplication, where through the principle of gene amplification, novel gene functions are discovered within genes with weak- or secondary protein functions. Subsequently, the novel function is maintained by selection and eventually optimized. Finally, we discuss a possible synergic link between lateral transfer and duplicative processes in gene innovation.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2003. 45 p.
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 796
Keyword
Bioinformatics, Bioinformatik
National Category
Bioinformatics and Systems Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:uu:diva-3283 (URN)91-554-5510-7 (ISBN)
Public defence
2003-02-21, Linddahlssalen, EBC, Uppsala, 13:00
Opponent
Available from: 2003-01-29 Created: 2003-01-29Bibliographically approved

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